The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Provides information about well-established PTMs for any target protein.
Entrez - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
ModPred is a sequence-based predictor of potential post-translational modification (PTM) sites in proteins. It consists of 34 ensembles of logistic regression models, trained separately on a combined set of 126,036 non-redundant experimentally verified sites for 23 different modifications, obtained from public databases and an ad-hoc literature search.
Find the latest high impact articles from the Cell family of journals about an assortment of PTMs. For the latest research on specific PTMs please see the links below.
CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs).
ExPASY has an array of protein modification resource tools.
The PTM Statistics Curator is an automated computational method for quantifying the number of each post-translational modification reported experimentally and non-experimentally in the Swiss-Prot Knowledgebase. Non-experimental qualifiers (Potential, Probable, By Similarity) are consistent with those defined in Swiss-Prot.
SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools.
Find the latest high impact articles and reviews from an array of journals about the protein modification, Acetylation.
Find the latest high impact articles from the Cell family of journals about the protein modification, Acetylation.
WERAM 1.0 is a comprehensive Eukaryotic Writers, Erasers and Readers protein of Histone Acetylation and Methylation system Database for 148 eukaryotic species.
Lysine acetylation is one of the important post-translational modifications of both histone and non-histone proteins. Thousands of acetylated proteins are known. However, few lysine acetylation transferases (KAT) responsible for the acetylation of these proteins have been identified. ASEB developed the Acetylation Set Enrichment-Based (ASEB) method to predict the KAT families responsible for a given protein.
Reversible acetylation on lysine residues, a crucial post-translational modification (PTM) for both histone and non-histone proteins, governs many central cellular processes. Due to limited data and lack of a clear acetylation consensus sequence, little research has focused on prediction of lysine acetylation sites. Incorporating almost all currently available lysine acetylation information, and using the support vector machine (SVM) method along with coding schema for protein sequence coupling patterns, we propose here a novel lysine acetylation prediction algorithm: LysAcet.
Find the latest high impact articles and reviews from an array of journals about the protein modification, Phosphorylation.
Find the latest high impact articles from the Cell family of journals about the protein modification, Phosphorylation.
PhosphoELM is a database of S/T/Y phosphorylation sites.
RegPhos is a resource to explore the protein kinase-substrate phosphorylation networks in human and mouse.
NetworKIN is a database that allows for the exploration of cellular phosphorylation networks.
GPS 3.0 with novel Peptide Selection and Weight Training methods to improve the prediction performance and robustness. Additionally, more than 6,000 phosphorylation sites were used for training and could predict kinase-specific phosphorylation sites for 464 human PKs in hierarchy.
Find the latest high impact articles and reviews from an array of journals about the protein modification, SUMOylation.
Find the latest high impact articles from the Cell family of journals about the protein modification, SUMOylation.
Improved prediction algorithm with added, novel SIMs prediction feature.
Uses a scoring system based on a position frequency matrix derived from the alignment of experimental SUMOylation sites or SUMO-interacting motifs (SIMs).
Find the latest high impact articles and reviews from an array of journals about the protein modification, Ubiquitylation (Ubiquitination).
Find the latest high impact articles from the Cell family of journals about the protein modification, Ubiquitination.
hUbiquitome is a public resource for the retrieval of experimentally verified human ubiquination enzymes and substrates. It is the first comprehensive database of human ubiqutitination pathway proteins and ubiquitin binding-site sequences which is freely available to academia.
UbiNet is a knowledge-based system that could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities.
UbPred is a random forest-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of 266 non-redundant experimentally verified ubiquitination sites available from our experiments and from two large-scale proteomics studies (Hitchcock, et al., 2003; Peng, et al., 2003).
Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. In fact, some sites that undergo ubiquitination have not been identified. In this work, we propose an evolutionary screening algorithm (ESA) to select effective negatives from among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy, better than existing prediction methods.